Colin Kaepernick’s success as 49ers QB likely signals the end for Alex Smith

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Colin Kaepernick, right, started as the 49ers QB on Sunday against the New Orleans Saints despite veteran Alex Smith being healthy enough to play.

This is probably the right time to take off that Alex Smith jersey and stuff it into a box with the rest of your 49ers memorabilia. Smith is still pacing the sideline in his red-and-gold helmet, but he’s practically a relic in the wake of Colin Kaepernick’s performance in a 31-21 victory over the New Orleans Saints on Sunday.

Last week, the idea that Kaepernick could replace a quarterback who led the 49ers to a 13-3 record and an appearance in the NFC Championship Game just a year ago seemed asinine. Smith is leading the NFL in completion percentage, he’s fifth in passing efficiency, and last season he set a 49ers record for fewest interceptions.

On the surface, this quarterback controversy appeared to be nothing more than sports radio fodder.

How could you replace a guy who beat the Saints in the NFC playoffs with a quarterback who’s started a grand total of one game?

"Some media pundits have provided the best answer to this question: Jim Harbaugh has observed a much bigger sample size than the rest of the football-loving public, and think Kaepernick gives his team the best chance of winning a Super Bowl."

While Harbaugh’s been a great mentor to Smith, the former No. 1 pick was never his top choice. Harbaugh moved up in the 2011 draft to nab Kaepernick with the 36th pick, and he courted Peyton Manning last offseason before re-signing Smith in March.

While Kaepernick was hardly perfect against the Saints (the 49ers should have scored more than two offensive touchdowns against the league’s worst defense), he showed us why Harbaugh has probably been planning to make this move for some time.

Once again, Kaepernick’s superior arm strength was on display. He stepped up and zipped a fastball to Delanie Walker for a gain of 25 on a crucial third-and-10 in the fourth quarter, a play Smith might not have been able to make.

But it isn’t just Kaepernick’s rocket arm that sets him apart from Smith; his athleticism brings more versatility to the offense, too. Although Smith was a good option quarterback in college, Kaepernick runs with the swiftness and the explosiveness of a tailback. He was barely touched on his seven-yard, read-option touchdown run in the first quarter, and later he juked out Saints defensive lineman Cameron Jordan to complete a 26-yard pass to Bruce Miller. In the second quarter, Kaepernick exploded up the middle for a 15-yard gain on third-and-seven.

Kaepernick, who finished 16-of-25 for 231 yards, one TD and one interception, also showed maturity in the second half, leading the 49ers on a 16-play, 85-yard field goal drive that consumed 9:28 of clock (the fourth-longest drive in the NFL this season), giving the team a 31-21 lead.

The second-year quarterback did display some youth when he threw into double coverage on a fumbled snap for his first interception of the season, but he didn’t allow the mistake to rattle him despite the noise in the Superdome.

Sure, Kaepernick could still get hurt or play himself out of the gig. Anything can happen, but it doesn’t seem likely. This is a move that Harbaugh’s been plotting for a while, and if he’s shown us anything, it’s that he rarely fumbles the ball.

Paul Gackle is a freelance writer and regular contributor to The San Francisco Examiner. He can be reached at paul.gackle@gmail.com and followed on Twitter @PGackle.